Arioch's comments (see Squat thread on the PL board) are pertaining to the tibiofemoral joint. Compressive forces on the PATELLOFEMORAL joint absolutely increase as the degree of knee flexion increases--there's some complex biomechanics here, but the most basic and common sense approach is that the further the quadriceps is stretched, as three of the four muscles are in the deep knee flexion required for a very low squat, the harder the patella is pressed against the femur. In a loaded position (body weight or with added resistance), the quads have to contract as well as lengthen in an eccentric contraction, shooting the PATELLOFEMORAL forces even higher. Over time, this high amount of force can, and does in many cases, wear away the articular cartilage on the back side of the patella.
But, as for stability, all 4 ligaments in the knee are slack at 90 degrees of flexion--and they remain slackened throughout any increase in knee flexion--just a biomechanical fact of life. The hamstring contraction does provide dynamic stability, but does not exactly duplicate the action of the ACL, nor does it come
close to duplicating the actions of the PCL, MCL, or LCL. So, ligamentous stability of the knee is decreased at flexion angles of 90 degrees or greater.
Again, I'm not saying that deep squats are a no-no for everybody. I am saying that to look strictly at the tibiofemoral joint as the only area of concern is just a partial picture of what happens in the knee joint complex during this activity.
And, I'm saying that there are a significant part of the exercising population for whom deep squats are inappropriate due to a history of patellofemoral joint problems and/or cartilage damage.
I go back to the statement "No exercise is contraindicated for everybody and no exercise is safe for everybody". If deep squats don't bother your knees and you have no concerns regarding excessive wear on patellar cartilage, do 'em til the cows come home. Otherwise, limit the frequency of deep squatting, or pass on it entirely and instead challenge the hip musculature with isolation exercises and keep the squats in the pain free range.